We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4) Ha/Bohr.
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http://dx.doi.org/10.1103/PhysRevLett.112.046401 | DOI Listing |
Sci Rep
December 2024
Department of Chemical and Biological Engineering, Gachon University, Seongnam, 13120, Republic of Korea.
The Crimean Congo virus has been reported to be a part of the spherical RNA-enveloped viruses from the Bunyaviridae family. Crimean Congo fever (CCHF) is a fatal disease with having fatality rate of up to 40%. It is declared endemic by the World Health Organization.
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December 2024
Department of Neuroscience and Padova Neuroscience Center, Università di Padova, Padova, Italy.
Can focal brain lesions, such as those caused by stroke, disrupt critical brain dynamics? What biological mechanisms drive its recovery? In a recent study, we showed that focal lesions generate a sub-critical state that recovers over time in parallel with behavior (Rocha et al., Nat. Commun.
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December 2024
Department of Clinical Pharmacy, Baoshan Hospital Affiliated to, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
This study investigates the potential treatment of breast cancer utilizing Gentiana robusta King ex Hook. f. (QJ) through an integrated approach involving network pharmacology, molecular docking, and molecular dynamics simulation.
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December 2024
Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
The Epstein-Barr virus (EBV) is widespread and has been related to a variety of malignancies as well as infectious mononucleosis. Despite the lack of a vaccination, antiviral medications offer some therapy alternatives. The EBV BZLF1 gene significantly impacts viral replication and infection severity.
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December 2024
Department of Chemistry, Illinois State University, Normal, IL, 61790-4160, USA.
This work aims to address key issues in the ballistic performance of ceramic-based composite armor, particularly at the joints of spliced bulletproof panels. The edge structure of C/C-SiC ceramic plates and ultra-high molecular weight polyethylene is redesigned to superimpose the joint areas. These structurally optimized composite pads are examined by numerical simulation of impact dynamics to understand their anti-penetration performance whose accuracy is then validated by live fire tests.
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